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226 Cards in this Set

  • Front
  • Back
Template Strand
Original Strand
complementary strand
new strand
Phosphorylated
molecules that have phosphate groups attached in a certain way; the addition of one or more phosphate groups raises the potential energy of the substrate molecules enough to make an endergonic reaction possible
Meiosis
Leads to the production of sperm and egg cells
DNA- RNA contrasts
2 aspects: sugar in DNA's backbone is deoxyribose instead of the ribose in RNA, and RNA contains the nitrogenous base uracil instead of the thymine found in DNA
Mitosis
division of the genetic material that produces daughter cells that are genetically identical to their parent cell
Mitosis and cytokinesis are responsible for what three key events in multicellular eukaryotes?
1. growth
2. repair
3. reproduction
Mitotic "M" phase
Dividing phase
Synthesis "S" phase
DNA synthesis
S phase is part of interphase
Cell Cycle
1. replication/ copying of hereditary material in chromosomes
2. partitioning of copied chromosomes to the two daughter cells during M phase

the hereditary material is duplicated, with one copy going to each daughter cell during mitosis. As a result, daughter cells contain genetic information identical to that of the parent cell
G1 phase and G2 phase
Why?
G1:occurs after M phase but before S phase
G2:occurs after S phase and before M phase
Why?:to replicate organelles and manufacture additional cytoplasm; before mitosis can take place, the parent cell must grow large enough and synthesize enough organelles that its daughter cells will be normal in size and function allowing the cell to complete all requirements for cell division other than chromosome replication
chromatid
each of the DNA copies in a replicated chromosome
Sister Chromatids
Chromatids from the same chromosome; identical in DNA content
interphase
After chromosome replication, each chromosome is composed of two sister chromatids. Centrosomes have replicated
**nondividing phase
"between phase"
Prophase
Chromosomes condense, and mitotic spindle begins to form
Prometaphase
Nuclear envelope breaks down. Spindle fibers contact chromosomes as kinetochore.
Metaphase
Chromosomes complete migration to middle of cell
Anaphase
Sister chromatids separate. Chromosomes are pulled to opposite poles of the cell.
Telophase
The nuclear envelope reforms, and the spindle apparatus disintigrates
Cytokinesis 1
Cell division begins: Actin-myosin ring causes the plasma membrane to begin pinching in
Cytokinesis 2
Cell division is complete: Two daughter cells form
Mitotic Spindle
A structure that produces mechanical forces that pull chromosomes into the daughter cells during mitosis; consists of microtubules
Spindle fibers
Groups of microtubules that attach to the chromosomes
Centrosome
Microtubule organizing center--a structure that contains a pair of centrioles
Cleavage furrow
In animals, fungi, and slime molds, cytokinesis begins with the formation of a cleavage furrow
Do regulatory molecules control entry into specific phases of the cell cycle?
M-phase cytoplasm contains a regulatory molecule that induces M phase in interphase cells
How to microtubules shorten to pull sister chromatids apart at anaphase?
Microtubules shorten at one end--at the kinetochore
How long does S phase last?
S phase is about 8 hours long. More important, there is a gap between S phase and M phase
Protein Kinase
An enzyme that catalyzes the transfer of a phosphate group from ATP to a target protein; one of the subunits of MPF
Mitosis-promoting factor (MPF)
Subsequent experiments showed that MPF induces mitosis in all eukaryotes
G1 checkpoint
Pass this checkpoint if:
-nutrients are sufficient
-growth factors (signals from other cells) are present
-cell size is adequate
-DNA is undamaged
G2 checkpoint
Pass this checkpoint if:
-chromosome replication is successfully completed
-no DNA damage
-activated MPF present
Metaphase checkpoint
Pass this checkpoint if:
-all chromosomes are attached to the mitotic spindle
Cancer
Arise from cells in which cell-cycle checkpoints have failed:
1. defects that make the proteins required for cell growth active at all times
2. defects that prevent tumor suppressor genes from shutting down the cell cycle

UNCONTROLLABLE DIVISION
INVADES NEARBY TISSUE
Growth factors
Polypeptides or small proteins that are responsible for stimulating cell division
Gametes
egg and sperm cells
Embryo
All the cells in a newly growing offspring
Sex Chromosome
"X" & "Y"
Autosome
All other chromosomes; non-sex chromosomes
Homologous Chromosomes
"homologs"
same proportion; have the same size and shape, carry the same genes, BUT each homolog may contain different alleles
Allele
different versions of the same gene
Gene
A segment of DNA that influences one or more hereditary traits in an individual
Ploidy
The number of each type of chromosome present; equivalent to the number of haploid chromosomes present; humans are 2n (diploid)
Zygote
The cell that results from fertilization and is diploid
Tetrad
Homologous chromosomes that have joined together
Early Prophase 1
(MEIOSIS 1)
Chromosomes condense, nuclear envelope breaks up, spindle apparatus forms. Synapsis of homologous chromosomes.
Late Prophase 1
(MEIOSIS 1)
Crossing over of non-sister chromatids (often multiple cross-overs between the same chromatids)
Metaphase 1
(MEIOSIS 1)
Tetrads migrate to metaphase plate
Anaphase 1
(MEIOSIS 1)
Homologs separate and begin moving to opposite sides of cell
Telophase and Cytokinesis 1
(MEIOSIS 1)
Chromosomes move to opposite sides of cell, then cell divides
Prophase 2
(MEIOSIS 2)
Spindle apparatus forms
Metaphase 2
(MEIOSIS 2)
Chromosomes line up at middle of cell (metaphase plate)
Anaphase 2
(MEIOSIS 2)
Sister chromatids separate, begin moving to opposite sides of cell
Telophase 2 and Cytokinesis
Chromosomes move to opposite sides of cell, then cell divides
Genetic recombination
Any change in the combination of alleles on a given chromosome
Crossing Over
Produces new combinations of alleles on the same chromosome--combinations that did not exist in either parent; recombination
Non-disjunction
Each pair of homologous chromosomes must separate from each other during the first meiotic division, so that only one homolog ends up in each daughter cell. If both homologs move to the same pole of the parent cell, the products of meiosis will be abnormal
Why does sexual reproduction occur?
Sexual reproduction is common in habitats where parasitism is common. Asexual reproduction is common in habitats where parasitism is rare.
Aneuploid
Cells that have too many or too few chromosomes
"without form"
Trisomy
Presence of an extra copy of a chromosome--because each cell has three copies of a chromosome (2n + 1)
What would you predict would happen to plant growth as carbon dioxide concentration increase?
Growth would increase because CO2 is an input to the Calvin cycle OR growth would decrease because STOMATA would remain open too long and the plant would dry out
What does hereditary material have to do?
1. Stores info for cell structure, function, development
2. replicates accurately
3. be capable of variation
Is hereditary information protein or DNA?
chromosomes contain both protein and DNA; however a series of experiments showed that DNA can transfer information from one cell to another and protein can't
Four bases
cytosine, thymine (pyrimidines)
guanine adenine (purines)
*held by hydrogen bonds
DNA
deoxyribonucleic acid
1. Double-stranded
2. Double helix
3. Complementary base pairing
4. Antiparallel strands
5. Sugar-phosphate backbone
6. Major and minor grooves
7. Gene regulatory proteins bind in grooves
Proto-oncogenes
(accelerator)
Normal genes produce proteins that trigger checkpoint passage; encourage cell growth oncogenes: mutated proto-oncogenes produce excess or super active protein
Tumor-suppressor genes
(brakes)
normal genes stop or slow the cell cycle and prevent cell cycle progression unless conditions are right; mutated tumor-suppressor genes fail to slow the cell cycle
Growth factor
protein that stimulates cell growth
*proto-oncogenes stimulate cell growth
Growth factor receptor
membrane protein; binds growth factors; stimulates a signal pathway that causes cell proliferation (Rapid increase in numbers)
Diploid cells
somatic cells, 2 sets of chromosomes
Haploid
eggs and sperm, one set of chromosomes
Cytokinesis in Plant cells
Lack centrioles and cytokinesis involves cell plate
Fanconi Anemia
-A disease of DNA repair and cancer
-most common inherited bone marrow failure disease
---RBCs
---WBCs
---platelets
-hypogonadism
-small head and small eyes
-squamous cell carcinoma of head and neck
-patients have DNA interstrand crosslinks they can't repair
Chromosome
A single DNA duplex wrapped around proteins
Telomeres
Ends of chromosomes
Transcription
makes an RNA copy from a DNA template
Translation
copies information in mRNA into the order of amino acids in a polypeptide
Where is transcription and translation performed in a eukaryotic cell?
Transcription is in the nucleus and translation is on cytoplasmic ribosomes (prokaryotes are simultaneous)
Gene structure
enhancers, promotors, exons, and introns
mRNA processing
intron removal, & 5' cap & 3' cap poly-A tail
Polypeptide
String of amino acids
Joined by peptide bonds
Order of amino acids determines shape
Shape determines function
How does DNA code for protein?
DNA nucleotide language--> transcription--> RNA nucleotide language--> translation--> amino acid language--> protein
mRNA
messenger RNA
encodes proteins
tRNA
transfer RNA
transfers amino acids
rRNA
ribosomal RNA
helps form the ribosome
Protein Synthesis: transcription: DNA to mRNA
Purpose? Where? Structures? Events?
Purpose: to make an RNA copy of a gene
Where: nucleus in eukaryotes; cytoplasm in prokaryotes
Structures: DNA, RNA nucleotides, RNA polymerase
Events: initiation, elongation, termination
Transcription: elongation
RNA polymerase moves along DNA template adding ribonuclotides (A to U, G to C)
Codon
Three nucleotides in mRNA corresponding to an amino acid in a polypeptide
Mutation
a change in nucleotide sequence
Transcription: initiation
promotor sequence to which RNA polymerase binds; RNA pol binds promotor and separates DNA strands
Transcription: termination
RNA polymerase falls off, RNA separates from DNA
RNA processing: pre-mRNA to mature mRNA (eukaryotes only)
Purpose? Where? Structures involved? Events?
Purpose: modify pre-mRNA for better stability and translation
Where: nucleus in eukaryotes
Structures involved: pre-mRNA, exons, introns, spliceosomes
Events: addition of 5' cap, addition of poly-A tail, splicing of introns
Exons
expressed in the mature mRNA
Introns
intervening in the gene but don't appear in mature mRNA (spliced out)
RNA splicing: eukaryotic cells only
Purpose? Where? Structures involved? Events?
Purpose: removal of introns
Where: nucleus in eukaryotes
Structures involved: primary transcript, spliceosomes, snRNPs
Events: snRNPs form spliceosome, remove intron
snRNPs
small nuclear riboproteins
Why can't eukaryotic cells have simultaneous transcription and translation like prokaryotic cells?
Prokaryotes don't have a nuclear envelope
Could one nucleotide encode one amino acid? Two? Three?
THREE...
Yes, you could encode 64 amino acid sequences, enough to encode the 20 commonly found in proteins
Substitution mutations
Can be silent, cause missense, or nonsense
Which end of the polypeptide is the N (amino) terminus?
distal end (furthest from mRNA)
You are a ribosome...
How do you know where to join the mRNA?
start codon!
You are a ribosome...
How do you know where to start translating the mRNA?
more of the mRNA sequence for CFTR
You are a ribosome...
How do you know when to stop translating?
Stop codon!
The mRNA encoding CFTR is 6129 base pairs long plus a poly-A tail of variable length. What is the maximum number of amino acids the CFTR protein could have?
2042
Max aa = max # of codons = (6129/3 - 1 stop codon)
CFTR protein is 1480 rather than 2042 aa long. What causes the protein to be shorter than predicted?
the mRNA includes 5' and 3' untranslated regions
UNTRANSLATED
Fertilization
doubles chromosome number from haploid to diploid
Silent Mutation
no change in protein sequence
Missense Mutation
changes protein sequence, so might change phenotype
Nonsense Mutation
Short protein, likely deleterious
Induces a stop codon
Frame Shift
Massive missense likely deleterious
Almost every cell in your body contains the same DNA. Why does the mutant CRTR gene only affect airways, pancreatic duct, sperm duct?
Different cells use different genes
Only duct cells rely heavily on CFTR to move chloride across the membrane
What makes muscles form?
notochord secretes "sonic hedgehog" protein
nearby cells respond by making muscle
Down Syndrome
Results from nondisjunction in meiosis 1 or meiosis 2
chromosome trisomy: 3 copies of chromosome 21
Karyotype
Ordered display of a cell's chromosomes
Number and types of chromosomes present
At what point in meiosis do cells first become haploid?
At the end of telophase 1
Genetic variation
-differences in genotype
-arises initially from mutation
1. independent assortment
2. fertilization
3. crossing over
Meiosis and Spermatogenesis
-sperm formation starts at puberty and continues throughout a man's life
-each meiotic cycle results in 4 sperm
-sperm live just a few days
Meiosis and Oogenesis
-each meiotic cycle results in one egg plus polar bodies
-conserves large cell size
-ovulation triggers completion of meiosis 1
-fertilization triggers completion of meiosis 2
-primary oocytes present BEFORE birth
If you ovulate today, how long has that cell been in meiosis 1?
Since before you were an embryo
Does the transforming factor consist of protein, RNA, or DNA?
DNA is the transforming factor
Do viral genes consist of DNA or protein?
Viral genes consist of DNA
Viral coats consist of protein
Genome
Entire complement of DNA
Is replication semiconservative, conservative, or dispersive?
Semiconservative: each newly made DNA molecule is comprised of one old strand and one new strand
RNA polymerase
Enzyme that catalyzes the synthesis of RNA; polymerizes ribonucleotides into strands of RNA (does not require a primer to begin adding ribonucleotides to a growing strand of RNA)
Genetic Code
The rules that specify the relationship between a sequence of nucleotides in DNA or RNA and the sequence of amino acids in a protein
**relates nucleotides to amino acids
Myc is a protooncogene found in humans that codes for a protein involved in regulating the cell cycle. When Myc is mutated, it may become an oncogene and lead to cancer. What is the specific role of Myc in regulating the cell cycle?
Since Myc is a protooncogene, it’s job is to stimulate cell growth by triggering specific phases of the cell cycle
Explain why a mutation in Myc may lead to cancer. Include in your answer a definition of cancer.
if Myc is mutated in a way that causes more of it’s product to be produced, or for Myc to produce a superactive product, cells may divide uncontrollably. If these cells that are growing uncontrollably invade nearby tissue, cancer may develop.
The protein coded for by Myc has 454 amino acids. Explain the difference between your answer 630 and the actual number of amino acids (454) in this protein.
the 5’ and 3’ untranslated regions + the 3’ poly-A tail account for this difference ; the mature mRNA has sequences on both the 5’ and 3’ end that do not get translated, and thus do not code for amino acids
We discussed cases of breast cancer that involve an increased number of copies of the gene that codes for the growth factor receptor HER2. In these cases, patients have receptors on the surface of breast cells that signal the tumor cells to divide even in the absence of a growth factor. Some patients with this form of breast cancer are given the chemotherapy drug Paclitaxel. Paclitaxel binds to microtubules and so interferes with their normal function during cell division. Which two stages of the cell cycle would you expect Paclitaxel to have the strongest effect? Justify your answers
microtubules are essential for the proper alignment of chromosomes on the metaphase plate during metaphase and the separation of sister chromatids during anaphase; without the proper movement of chromosomes directed by microtubules, cell division will not occur correctly
Suppose another type of chemotherapy drug interferes with the normal functioning of DNA polymerase. Which stage of the cell cycle would this drug have the strongest effect and why would this drug be an effective therapy against cancer? Explain.
if DNA polymerase is not functioning properly, DNA replication, or the S phase,will not occur correctly during cell division since DNA polymerase is the enzyme responsible for synthesizing DNA during replication; this drug will be effective because without DNA replication occurring properly, the cell will not proceed through the rest of the cell cycle
Neimann-Pick disease is a lysosomal storage disease that can lead to the toxic accumulation of lipids in the spleen, liver, lungs, bone marrow, and brain. Mutations in the SMPD1 gene cause Neimann-Pick disease. What specific type of molecule must the SMPD1 gene code for?
enzyme
Penetrance
of individuals with the genotype, the % that show the phenotype
Expressivity
the severity of the condition (penetrance)
Complex Traits
involve several interacting genes that often interact with the environment
the analysis of complex traits is an important but daunting task for human medical genetics
heart disease, autism, asthma, diabetes, cancers, schizophrenia
Sex-limited traits
more likely to be found in one sex than another, and may be autosomal or sex linked
Pleiotropy
one gene affects several phenotypes
What are the benefits and risk of using GENETIC SCREENING for the presence of the BRCA genes?
-negative tests may give a FALSE SENSE OF SECURITY and/or SURVIVAL GUILT
-some positive people don't get disease or get it very late in life (but 56-85% penetrance)
-PROPHYLACTIC MASTECTOMY reduced cancer incidence by 90%
-finding out about gene can give information about family members
-how do you safeguard records from insurance companies?
What does your mother give you that your father does not?
mother gives you your cytoplasm which contains all your organelles

in mitosis, mitochondria randomly distribute to daughter cells which accounts for the variability of the disorder
Y-chromosomes have few....?
...genes that affect phenotypes other than male development
Rare traits
it is unlikely that members of a family in which a trait is segregating will have children with people who carry the same rare trait
A colorblind woman marries a man with normal vision. What are the expected phenotypes and ratios of their offspring?
daughters all normal vision, sons all colorblind
If two parents do not show a trait, and their child displays the trait... then the trait is..?
recessive
A man with a rare genetic trait marries a woman who does not have this condition. They have three children. The first is a daughter who has the trait. The second is a daughter without the trait. The third is a son without the trait. What is the most likely mode of inheritance of this trait. Support your answer by giving genotypes of all individuals and a short written justification.
X-linked recessive?
works, but requires that both mom and dad carry a rare allele which is unlikely
autosomal recessive?
works, but requires the affected person to select a mate that's a heterozygote which is unlikely
autosomal dominant?
YES; does work and doesn't require unlikely mating like autosomal recessive does
Sex Chromosomes
Pair in meiosis but differ between sexes
Autosomes
Pair in meiosis but do not differ between sexes
Humans have 22 pairs of autosomes and one pair of sex chromosomes = 23 pairs of chromosomes total
X-chromosome inactivation
equalizes gene dosage in males and females and is evident in a Barr body
Barr body
inactivated X chromosome
random inactivation of maternal X or paternal X during early development
thus, gene dose of XX female and XY male is the same
Most human females have a condensed clump of chromosomal material called a Barr Body along the nuclear envelope in body cells in interphase of the cell cycle.
What is the rule for the number of Barr Bodies per cell?
Number of Barr Bodies = # of X's-1
SRY gene
encodes a transcription factor
SRY binds to specific DNA sequence and bends it
causes testis development in mammals
How could Maria have testosterone but not show its effects?
she lacks the receptor
Incomplete dominance
the phenotype of the heterozygote is intermediate between the phenotypes of the two heterozygotes
Co-dominance
heterozygotes show characteristics of both homozygotes in full form; usually structure of protein or DNA
What makes a mutation dominant or recessive or incomplete or co-dominant?
the binding of enzymes and growth factor receptors
Frequency of recombinants
50% frequency of recombinants means independent assortment; less than 50% recombinants means linked genes
Genetic maps
reveal that genes are arranges in a linear order along the chromosome
Crossing over frequency
increases with distance
genes on same chromosome can be so close they have nearly 0% recombinants
genes on same chromosome can be so distant they have nearly 50% recombinants
Linked genes
tend to stay together in meiosis because they lie close together on the same chromosome
Crossing-over
of linked genes can change allele combinations
results in recombinant combinations
Parental Alleles
allele combinations that remain unchanged through meiosis; recombinant combinations result from crossing over
Frequency of recombinants/Map distance
sum of recombinants divided by total progeny
the frequency of recombinants gives the map distance
map distance varies between zero and 50%
In a pedigree for a ________, affected children can have unaffected parents
recessive trait
In a pedigree for a _________, affected children have at least one affected parent
dominant trait
(with the exception of new mutations)
A purebred purple wrinkled parent is bred to a purebred yellow round parent to produce F1’s. All F1s are purple round.
P > y & R > w
The F1 is bred with a yellow wrinkled individual to give F2’s. Assume the color gene and shape gene are close together on the same chromosome.
What are the genotypes of the parents in the parental
generation?
PPww × yyRR
How would you determine whether the observed results are as expected from the independent assortment hypothesis?
You would do a Chi-square analysis to obtain the probability that the results (97:398:103:402) is statistically different from a 1:1:1:1 ratio.
How can you explain the fact that the results are not exactly as expected from either the independent assortment hypothesis or the close neighbor hypothesis?
The two genes must be linked on the same chromosome, because the results are intermediate between what you would expect for independent assortment and what you’d expect from tightly linked genes.
Woody’s genotype: HN HD
Woody produced sperm by the process of meiosis. Considering the H gene, how many different genotypes of sperm did Woody produce, and in what ratios?
Two genotypes, HN and HD in a 1:1 ratio
If a man that is heterozygous for both achondroplasia and neurofibromatosis marries a woman who is also heterozygous for both achondroplasia and neurofibromatosis, what would be the expected phenotypes and ratios of their surviving offspring? Show your work in the space below. Hint: a punnett square may be helpful!
4:2:2:1 (achondroplastic dwarfism/neurofibromatosis : normal height/neurofibromatosis : achondroplastic dwarfism/normal skin :normal height/normal skin) (7 dead offspring)
The following questions refer to human germ-line cells undergoing meiosis. Remember that the 2N (diploid) number for humans is 46.
How many molecules of DNA are in a single human cell in Meiosis prophase 1?
How many molecules of DNA are in a single human cell in Meiosis prophase 2?
Are chromosomes duplicated or unduplicated in Meiosis prophase 2?
92
46
duplicated
Broccoli (yum!) cells have a total of 18 chromosomes (9 from mom broccoli & 9 from dad broccoli). Answer the following questions and then draw a broccoli cell in anaphase in the circle below.
How many molecules of DNA are in the nucleus of a broccoli cell during G1?
How many molecules of DNA are in the nucleus of a broccoli cell during metaphase?
18
36
Many drugs used in cancer treatment interfere in some way with mitosis. Vinblastine is a drug that prevents cells from forming spindle fibers. On which stage of mitosis should this drug have the largest effect? Justify your answer.
Metaphase is the best answer since the chromosomes will not be able to line up on the metaphase plate without the spindle fibers; prophase is also be acceptable since it is during this stage that the spindle apparatus begins to form.
A mutation is any permanent change in an organism’s DNA. A mutation may be harmful, beneficial, or neutral in its effect on an individual’s phenotype. When a mutation is neutral, there is no change in the phenotype (the way an individual looks and functions). Provide two explanations for why a mutation might not alter the phenotype.
The mutation might change a base in a codon position that does not change the amino acid (redundancy of the genetic code)
The mutation might change a base in a 3’ or 5’ untranslated region or an intron
also acceptable: the mutation might change the amino acid sequence but the change might not disrupt the shape and function of the protein
When the lights are on, the concentration of NADP+ is about the same as the concentration of NADPH in a chloroplast. What would happen to the concentration of these two molecules when the lights are turned off? Why?
NADP+ will go up but NADPH will go down.

Without light there is no more NADPH being produced via the light reactions. Any NADPH that is present would be oxidized to NADP+ in the Calvin cycle (which doesn’t need light). Eventually all of the NADPH would be converted to NADP+.
The compound PNO8 binds to and inhibits the portion of photosystem II labeled ‘PQ’ in the figure . You treat plant cells with PNO8. For each of the following processes, indicate if it could still occur immediately after the inhibitor takes effect. Then explain why or why not on a cellular/molecular level. You may need to consider events not depicted in the figure. (Eventually the cells would die and none of the following would occur. This question is asking what happens in the short term, immediately following the initiation of inhibitor function.)
Splitting of water to electrons, hydrogen ions, and oxygen.
If yes, then chlorophyll can still absorb light and emit electrons, but there would be no place for them to go in absence of active PQ; water could still be split to fill the electron hole in chlorophyll.
If no, then if PQ can’t take electrons, then there’s no place for electrons to go when chlorophyll emits light-excited electrons, so electrons don’t get boosted from chlorophyll and water is not split.
The compound PNO8 binds to and inhibits the portion of photosystem II labeled ‘PQ’ in the figure. You treat plant cells with PNO8. For each of the following processes, indicate if it could still occur immediately after the inhibitor takes effect. Then explain why or why not on a cellular/molecular level. You may need to consider events not depicted in the figure. (Eventually the cells would die and none of the following would occur. This question is asking what happens in the short term, immediately following the initiation of inhibitor function.)
Establishing a gradient of hydrogen ions across the thylakoid membrane.
Occur?
PQ must carry electrons to cytochrome to get H+ pumped across the membrane, and without hydrogen ion pumping, there will be no hydrogen ion gradient.
The compound PNO8 binds to and inhibits the portion of photosystem II labeled ‘PQ’ in the figure. You treat plant cells with PNO8. For each of the following processes, indicate if it could still occur immediately after the inhibitor takes effect. Then explain why or why not on a cellular/molecular level. You may need to consider events not depicted in the figure. (Eventually the cells would die and none of the following would occur. This question is asking what happens in the short term, immediately following the initiation of inhibitor function.)
Production of ATP.
Occur?
The hydrogen ion gradient is necessary to get ATP made. If no electron transport, no hydrogen ion gradient, and no hydrogen ions flowing through ATP synthase, then no ATP is made.
The compound PNO8 binds to and inhibits the portion of photosystem II labeled ‘PQ’ in the figure. You treat plant cells with PNO8. For each of the following processes, indicate if it could still occur immediately after the inhibitor takes effect. Then explain why or why not on a cellular/molecular level. You may need to consider events not depicted in the figure. (Eventually the cells would die and none of the following would occur. This question is asking what happens in the short term, immediately following the initiation of inhibitor function.)
Production of NADPH.
If yes, then NADPH is made by photosystem I, which is not affected initially and primarily by inhibition of PQ.
If no, then electrons going to reduce NADP+ to NADPH come from chlorophyll after light absorption in photosystem I, and those electrons are replaced by electrons from photosystem II. If photosystem II doesn’t work, then no electrons go to the chlorophyll in photosystem I, and so you’d get no NADPH
The compound PNO8 binds to and inhibits the portion of photosystem II labeled ‘PQ’ in the figure. You treat plant cells with PNO8. For each of the following processes, indicate if it could still occur immediately after the inhibitor takes effect. Then explain why or why not on a cellular/molecular level. You may need to consider events not depicted in the figure. (Eventually the cells would die and none of the following would occur. This question is asking what happens in the short term, immediately following the initiation of inhibitor function.)
Carbon dioxide fixation reactions of the Calvin cycle?
If yes, then the Calvin cycle will continue to work as long as there’s a supply of CO2, ATP, and NADPH. It won’t stop just because PQ doesn’t transfer electrons.
If no, then the Calvin cycle has to have ATP. If PQ doesn’t work, then the amount of ATP would go down and there wouldn’t be enough to run the Calvin cycle.

(INPUTS OF THE CALVIN CYCLE: CO2, ATP, NADPH)
To what kingdom do yeast belong?
fungi
You perform an experiment to investigate energy harvest in yeast. You put yeast cells in a closed beaker with a probe that measures the amount of carbon dioxide (CO2) in the beaker during the experiment. The experiment starts with 350 parts per million (ppm) of carbon dioxide. You conduct the first ten minutes of the experiment at room temperature (22° C), and then raise the temperature to 37°C, a temperature equal to human body temperature, for the second ten minutes (37°C is within the tolerance range of yeast enzymes). The amount of glucose in the beaker never limits yeast cell growth and plenty of oxygen is present in the beaker. Explain on a cellular/molecular level what is specifically responsible for any change in the amount of CO2 in the beaker during the first 10 minutes. List the specific names of any processes involved and exactly how carbon dioxide is involved in the process.
As a result of cellular respiration, CO2 is increasing in the beaker over time. Specifically, CO2 is a product of the Krebs Cycle and the conversion of pyruvate to acetyl CoA.
You perform an experiment to investigate energy harvest in yeast. You put yeast cells in a closed beaker with a probe that measures the amount of carbon dioxide (CO2) in the beaker during the experiment. The experiment starts with 350 parts per million (ppm) of carbon dioxide. You conduct the first ten minutes of the experiment at room temperature (22° C), and then raise the temperature to 37°C, a temperature equal to human body temperature, for the second ten minutes (37°C is within the tolerance range of yeast enzymes). The amount of glucose in the beaker never limits yeast cell growth and plenty of oxygen is present in the beaker.
Is there any difference in the slope of your graph in the first 10 minutes vs. the second 10 minutes? Explain why the slope did or did not change. Be sure your explanation includes a discussion of what is happening on a molecular level.
Yes, the amount of CO2 being produced increases when the temperature is raised from 22° C to 37°C. This happens because the enzymes that are essential for the reactions associated with cellular respiration are more active at 37°C than 22° C. Because the kinetic energy of the system, including substrate molecules, is greater, more successful substrate/enzyme collisions occur, and therefore the overall rate of reaction is increased.
You perform an experiment to investigate energy harvest in yeast. You put yeast cells in a closed beaker with a probe that measures the amount of carbon dioxide (CO2) in the beaker during the experiment. The experiment starts with 350 parts per million (ppm) of carbon dioxide. You conduct the first ten minutes of the experiment at room temperature (22° C), and then raise the temperature to 37°C, a temperature equal to human body temperature, for the second ten minutes (37°C is within the tolerance range of yeast enzymes). The amount of glucose in the beaker never limits yeast cell growth and plenty of oxygen is present in the beaker. Would your graph look any different if you were to conduct the same experiment but without oxygen in the beaker? Why or why not?
The graph will look similar because even without oxygen, yeast will produce CO2 as a result of alcohol fermentation. The overall amount of CO2 produced may be less so the slope will be lower, but CO2 will still be increasing.
Fabry’s disease patients lack the enzyme that normally degrades Gb3. From the list below, circle all of the organelles that are involved in the synthesis of the enzyme that degrades Gb3. For each organelle you circle, briefly explain it’s role in the production of the enzyme.
Nucleus:
Ribosome:
Golgi apparatus:
RER:
Nucleus: contains the gene, DNA, that encodes the enzyme
Ribosome: is the workbench upon which proteins, including the enzyme, are made
Golgi apparatus: adds tags (carbohydrates) to the enzyme that direct it to the lysosome
Rough endoplasmic reticulum: has the ribosomes on which the enzyme is synthesized; enzyme goes into the RER lumen
Mendel’s 1st law
Alleles segregate in meiosis, join randomly in fertilization •A chi-square test helps determine how likely an experimental result
deviates from expected solely by chance.
Females have 23 pairs of identical chromosomes..How many do males have?
22 pairs of identical chromosomes
because last pair (XY) are NOT identical pair
Chi-square test formula
x²= Σ(observed-expected)²/expected
You count your flies in lab, analyze the data, and calculate a X2 of 0.02 with 2 categories. Are your results consistent with Mendel?
A. Yes, because the probability that this would occur solely by chance is about 0.8 or so, 80%. B. Yes, because the probability that this would occur solely by chance is about 0.98 or so, 98%.
C. No, because the probability that this would occur solely by chance is about 0.8 or so, 80%. D. No, because the probability that this would occur solely by chance is about 0.02 or so, 2%.
E. Insufficient data to make a choice.
A. Yes, because the probability that this would occur solely by chance is about 0.8 or so, 80%.
Hunter syndrome is a genetic disorder that primarily affects males. The disease interferes with the body’s ability to break down and recycle a specific polysaccharide known as GAG. Physical symptoms associated with this disease include distinct facial features, a large head, and an enlarged abdomen. Other symptoms include hearing loss, thickening of heart valves, enlargement of liver and spleen and death by 15 years of age. If a woman has a son with Hunter syndrome, the likelihood another son is affected is 50%, but her daughters are virtually never affected.
What specific kind of macromolecule does the gene associated with Hunter syndrome code for?
Where and Why in the cell is the macromolecule you listed in part a most likely found?
enzyme
lysosome
lysosome is the recycling center of the cell; it contains enzymes that are responsible for breaking down old molecules and cell parts
In eukaryotes during photosynthesis, the concentration of H+ is made higher __________ than it is ________________________.
in the thylakoid space
in the stroma
In eukaryotes during cellular respiration, the concentration of H+ is made higher in the ____________ than it is ______________________________________
in the mitochondrial matrix
intermembrane space
Where does the energy come from during cellular respiration and in photosynthesis to create the H+ gradient?
movement of electrons through the ETC
Circle each of the following processes that is part of cellular respiration.
Krebs cycle
glycolysis
electron transport chain
regeneration of NAD+(as part of fermentation)
Krebs cycle
glycolysis
ETC
Circle each of the following processes that is part of fermentation.
Krebs cycle
glycolysis
electron transport chain
regeneration of NAD+(as part of fermentation)
glycolysis
regeneration of NAD+
Circle each of the following processes that produces ATP.
Krebs cycle
glycolysis
electron transport chain
regeneration of NAD+(as part of fermentation)
Krebs cycle
glycolysis
electron transport chain
Circle each of the following processes that occurs in the cytoplasm.
Krebs cycle
glycolysis
electron transport chain
regeneration of NAD+(as part of fermentation)
glycolysis
regeneration of NAD+
A mutation is discovered that changes the first T in the template strand of DNA into a G. What would be the effect of this mutation at the molecular level?
It destroys the start codon, thus there would be no protein made.
How would you determine whether the observed results are as expected from the independent assortment hypothesis?
Do a chi-square test to compare observed and expected numbers.
How can you explain the fact that the results are not exactly as expected from either the independent assortment hypothesis or the close neighbor hypothesis?
The two genes are on the same chromosome and are linked, but there are recombinants between them.
You observed the aquatic organism pictured here in the first lab of the term. It is single celled, has a nucleus, a flagellum that you can see at the left, chloroplasts (the oval shaped organelles), and mitochondria. It can engulf smaller organisms and ‘eat’ them for energy.
a. Which kingdom does it belong to?
b. Support your answer for part a.
c. You place an equal number of these organisms in water in each of two flasks with plenty of their food organism and plenty of carbon dioxide. You put flask A in the light and flask B in the dark. Both flasks start out with 20% oxygen at time zero.
On the graph here, draw a line to represent the change over time for each of the two flasks.
d. Explain why your graph lines look as they do.
a. protista or fungi
b. Nucleus means its a eukaryote. Single cell means its fungi or protista. (Flagellum means its not fungi, but I don’t know if we emphasized this).
d. In the light, photosynthesis produces oxygen faster than respiration uses it, in the dark, respiration uses oxygen faster than photosynthesis produces it.
BRCA1 is the most commonly mutated gene in familial breast cancer. The BRCA1 gene is 81,000 nucleotides long but its mRNA is only 5,693 nucleotides long.
a. What probably accounts for the difference in lengths of the BRCA1 gene and its mRNA
b. The BRCA1 protein is actually 1863 amino acid residues long. If there is a difference between your answer for 1b and the actual length of BRCA1 protein, what accounts for that difference? If there is no difference, then explain the process that makes them the same length.
a. The gene includes introns that are spliced out of the primary transcript to make the mRNA.
b. the maximum length is longer than the actual length because the mRNA has untranslated regions (5’ and 3’)
Castilla et al. isolated DNA from tumors in two family members and found that the tumors had only the mutant (inactive) form of the BRCA1 gene. Does the normal version of BRCA1 speed or slow the growth of breast cells? Support your answer.
This tumor, without BRCA1 function, grows without ceasing, and so the normal BRCA1 protein must stop inappropriate growth.
Myc is a protooncogene found in humans that codes for a protein involved in regulating the cell
cycle. When Myc is mutated, it may become an oncogene and lead to cancer.
a. What is the specific role of Myc in regulating the cell cycle?
b. Explain why a mutation in Myc may lead to cancer. Include in your answer a definition of cancer.
c. The mature mRNA for Myc is 1,893 nucleotides long. What is the maximum number of amino acids expected to be in the protein? Show your work and explain your answer.
d. The protein coded for by Myc has 454 amino acids. Explain the difference between your answer for part c and the actual number of amino acids (454) in this protein.
a. Since Myc is a protooncogene, it’s job is to stimulate cell growth by triggering specific phases of the cell cycle
b. if Myc is mutated in a way that causes more of it’s product to be produced, or for Myc to produce a superactive product, cells may divide uncontrollably. If these cells that are growing uncontrollably invade nearby tissue, cancer may develop.
c. 1893/3 (since there are 3 mRNA bases per amino acid) = 631 - 1 amino acid since the stop codon does not code for an amino acid = a maximum of 630 amino acids
d. the 5’ and 3’ untranslated regions + the 3’ poly-A tail account for this difference ; the mature mRNA has sequences on both the 5’ and 3’ end that do not get translated, and thus do not code for amino acids
Suppose another type of chemotherapy drug interferes with the normal functioning of DNA polymerase. Which stage of the cell cycle would this drug have the strongest effect and why would this drug be an effective therapy against cancer? Explain.
if DNA polymerase is not functioning properly, DNA replication, or the S phase,will not occur correctly during cell division since DNA polymerase is the enzyme responsible for synthesizing DNA during replication; this drug will be effective because without DNA replication occurring properly, the cell will not proceed through the rest of the cell cycle
Pancreatic lipase (PNLIP) is the main enzyme responsible for breaking down triglycerides in the human digestive system. The pancreas secretes PNLIP into the small intestine, where most lipid digestion occurs.
a. Describe the steps pancreatic cells take to synthesize PNLIP. Start with DNA in the nucleus and end with the secretion of the enzyme from the cell. Organize your route by the steps below to facilitate grading but you can use fewer or more steps if needed. Mention some or all of the following cell parts in your explanation: rough endoplasmic reticulum (RER), smooth endoplasmic reticulum (SER), lysosome, cytoskeleton, nucleus, ribosomes, mRNA, DNA, Golgi apparatus (GA), transport vesicles, mitochondrion, chloroplast, cell wall, plasma membrane, vacuole. Answer must fit in space and be legible.
Step 1: In the nucleus, the PNLIP gene in DNA is read into mRNA, which exits the nucleus and joins onto ribosomes in the cytoplasm.
Step 2: Ribosomes join to the RER, produce the protein, which ends up in the lumen of the RER.
Step 3: Transport vesicles bud off from the RER and transport the nascent protein to the Golgi.
Step 4: Golgi apparatus adds to the protein carbohydrate tags that provide an address for sending to the plasma membrane.
Step 5: Transport vesicles bud off from the Golgi and transport the protein; they fuse with the plasma membrane, thus secreting the protein from the surface of the cell into the outside of the cell.
What type of macromolecule is a triglyceride?
lipid
What are the two molecular building blocks of a triglyceride?
glycerol + 3 fatty acids

(oh yeah that guy!)
How do you know an R-group in a monomer is polar, non-polar, acidic or basic?
Polar: because it has atoms such as oxygen and/or nitrogen atoms that would interact with water.
Non-polar: because it lacks highly polar atoms but has many CH₂ groups
Acidic: because it has an organic acid, a carboxyl group that can donate hydrogen ions.
Basic: because it has NH₂ groups that can accept Hydrogen ions.
Phospholipid bilayers do not usually allow hydrogen ions to cross. A drug called dinitrophenol (DNP) was once prescribed to help people lose weight, but it was later found to be unsafe. DNP acts by making the phospholipid bilayer of the inner mitochondrial membrane leaky to hydrogen ions.
a. Would the ability of the electron transport chain to pump hydrogen ions across the inner mitochondrial membrane increase or decrease in the presence of DNP?
b. Would the ability of cells to make NADH increase or decrease in the presence of DNP? (circle answer) Explain your reasoning using the diagram.
c. Would the ability of cells to make ATP from glucose increase or decrease in the presence of DNP?
a. It would stay the same, because DNP makes the membrane leaky, but the 1st, 3d, and 4th green proteins could still pump H+ ions; those H+ ions just would leak back across. Its like putting water into a leaky bucket – a leak in the bucket wouldn’t stop you from putting water in, it would just go out the leak.
b. NADH is made in glycolysis and the Krebs Cycle, processes that are not affected by the DNP and are far upstream of the action of DNP, so NADH synthesis would remain about the same.
c. Cells make large amounts of ATP by the flowing of H+ ions across the ATP synthase at the right of the figure. If the membrane leaks, then lots of H+ would flow through the leaks rather than through the ATP synthase, so much less ATP would be made.
Which organelle (or organelles) is shared by both plant and animal cells?
nucleus, cytoplasm, and mitochondria
In which organelle or organelles does the Calvin cycle take place?
Where sugar is produced?
stroma of chloroplast
Where is the location of the electron transport chain of PHOTOSYNTHESIS?
thylakoid membrane
Where are hydrogen ions are pumped in an electron transport chain?
intermembrane space of mitochodrian and lumen (inside) of thylakoid
Name the place where the most ATP is harvested from sugars
inner mitochondrial membrane
What is the condition for a cell to be in the Domain Eucarya?
Needs to have a nucleus
How does an enzyme cause a difference between a reaction that did not have an enzyme used?
The enzyme (1) decreases the activation energy, (2) brings substrates close together, (3) stresses their bonds, (4) making a favorable environment for the reaction and making an intermediate
Greg set up an experiment in which he grew pots of tomato plants in different chambers under light bulbs that emit different wavelengths, but the same intensity, of light. The bulb for Pot A emitted only blue light; the bulb for Pot B emitted only green light; the bulb for Pot C emitted only red light; and the bulb for Pot D emitted white light containing all visible wavelengths. All other conditions were the same for all pots and plants only received light from the bulb that they were placed under.
Rank the relative rates at which photosynthesis will proceed for the 4 plants grown in the experiment (1 is the fastest, 4 is the slowest).
(blue is better than red, but to know this you have to remember the absorption spectrum really very well, and that's not necessary)
Blue: 3 or 2
Green: 4
Red: 2 or 3
White: 1
Early onset Alzheimer’s disease is caused by mutation in the Presenilin-1 gene (PSEN1). The lipid bilayer of the plasma membrane is a final cellular location of the mature PSEN1 protein.

Explain the route of biosynthesis of the PSEN1 protein starting with DNA and ending at the plasma membrane. Mention some or all of the following cell parts in your explanation: rough endoplasmic reticulum (RER), smooth endoplasmic reticulum (SER), lysosome, cytoskeleton, nucleus, ribosomes, mRNA, DNA, Golgi apparatus (GA), transport vesicles, mitochondrion, chloroplast, cell wall, plasma membrane. Be concise.
Step 1: The PSEN1 gene in DNA in the NUCLEUS is copied into mRNA, which moves into the cytoplasm.
Step 2: The mRNA joins RIBOSOMES that go to the RER where the protein is translated and moves into the membrane of the RER
Step 3: The protein moves into TRANSPORT VESICLES that take it to the GOLGI APPARATUS
Step 4: The GOLGI modifies the protein and sorts it to TRANSPORT VESICLES that take it to the PLASMA MEMBRANE
Step 5: Could also add without penalty that the mitochondria provide the ATP for protein synthesis. Don’t take off if they tell correctly the functions of other structures
Brain cells in people with a mutation that destroys the function of PSEN1 accumulate a protein called A-beta and these brain cells die, leading to Alzheimers disease. People with a normal PSEN1 gene contain A-beta protein that is broken into two parts.
From this information, what can you infer about the job of normal PSEN1 protein in brain cells?
Normal PSEN1 must cause A-beta protein to be cleaved, and somehow, that stops A-beta accumulation and promotes brain cell survival.
What type of information would describe the primary structure of ANY protein
The order of amino acids
What represents the secondary structure of a protein?
alpha-helices and beta-sheets
What represents the tertiary structure of a protein?
The postition of the alpha-heices and the blue coils in 3-dimensional shape
What represents the quaternary structure of a protein?
The quaternary structure is the position of two or more polypeptides in space that make up a complete protein
A baby is born that has a mutation in a gene for complex IV in the ETC that causes this complex not to work when the baby eats food containing vitamin E.
How will levels of FAD in the baby's cells change after it eats vitamin E?
They will go down
If complex IV doesn't work, then there will be no electron transport, and so FADH₂ will not be converted to FAD and so the quantity of FAD in the cell will decrease as the Krebs cycle continues to make FADH₂ but the electron transport chain does not use it up
Is the reaction catalyzed by complex IV with water as a product of endergonic or exergonic reaction?
It is an exergonic reaction
The oxidation of hydrogen ions releases energy that is used to pump hydrogen ions across the membrane
The ETC allows hydrogene ions to accumulate on one side of the membrane. What will the cell use this hydrogen ion gradient for?
The hydrogen ion gradient is used to make ATP as the hydrogen ions flow back across the membrane through ATP synthase
You discover in the Millrace a single celled organism that has chloroplasts and a nucleus but no mitochondria or cell walls. Tell which kingdom(s) listed may possibly contain this organism and give reasoning to support your answer. For any kingdom(s) you rule out, very briefly explain what information allows you to rule out that kingdom.
Bacteria:
Archaea:
Fungi:
Protista:
Plants:
Animals:
Bacteria [No, because the organism has a nucleus but bacteria don’t.] Archaea [No, because the organism has a nucleus but archaea don’t.] Fungi [No, because the organism has chloroplasts but fungi don’t.] Protista [Yes, because some protists have all of these cell components.] Plants [No, because the organism is single celled and plants are multicellular.]
Animals [No, because the organism is single celled and has chloroplasts, but animals are multicellular and don’t have chloroplasts.]
Light capturing reactions of photosynthesis?
Calvin Cycle, Krebs Cycle, or both?
CALVINNNNN